#load packages
library(vcfR)
library(ggplot2)
library(adegenet)
library(SNPfiltR)
library(StAMPP)
#read in vcf as vcfR
#this has been pre-filtered using the command:
#vcftools --vcf populations.snps.vcf --out filt --max-missing .1 --recode --recode-INFO-all
#in order to make sure that the file can be read into Rstudio
vcfR <- read.vcfR("~/Desktop/todi.2022/populations.snps.vcf")
### check the metadata present in your vcf
vcfR
#read in sample info csv
sample.info<-read.csv("~/Desktop/todi.2022/todiramphus.subset.csv")
#make sure sampling file matches vcf
sample.info$id %in% colnames(vcfR@gt)[-1]
colnames(vcfR@gt)[-1] %in% sample.info$id
#if needed, subset sampling file to include only samples in vcf
#sample.info<-sample.info[sample.info$id %in% colnames(vcfR@gt)[-1],]
#reorder sampling file to match order of samples in vcf
sample.info<-sample.info[match(colnames(vcfR@gt)[-1], sample.info$id),]
sample.info$id == colnames(vcfR@gt)[-1]
#hard filter to minimum depth of 5, and minimum genotype quality of 30
vcfR<-hard_filter(vcfR=vcfR, depth = 5, gq = 30)
## 25.19% of genotypes fall below a read depth of 5 and were converted to NA
## 1.6% of genotypes fall below a genotype quality of 30 and were converted to NA
#execute allele balance filter
vcfR<-filter_allele_balance(vcfR)
## 9.4% of het genotypes (0.4% of all genotypes) fall outside of 0.25 - 0.75 allele balance ratio and were converted to NA
#visualize and pick appropriate max depth cutoff
max_depth(vcfR)
## cutoff is not specified, exploratory visualization will be generated.
## dashed line indicates a mean depth across all SNPs of 53.3
#filter vcf by the max depth cutoff you chose
vcfR<-max_depth(vcfR, maxdepth = 100)
## maxdepth cutoff is specified, filtered vcfR object will be returned
## 16.32% of SNPs were above a mean depth of 100 and were removed from the vcf
#check vcfR to see how many SNPs we have left
vcfR
## ***** Object of Class vcfR *****
## 100 samples
## 347 CHROMs
## 186,091 variants
## Object size: 346.7 Mb
## 83.77 percent missing data
## ***** ***** *****
#run function to visualize samples
miss<-missing_by_sample(vcfR=vcfR)
## No popmap provided
#histogram of number of SNPs called in each sample at a .5 SNP completeness cutoff
hist(miss$snps.retained[miss$filt == .5], breaks=50)
hist(miss$snps.retained[miss$filt == .5], breaks = 100)
#run function to drop samples above the threshold we want from the vcf
#(going with a very lenient cutoff here, can clean up bad samples down the line if needed)
vcfR<-missing_by_sample(vcfR=vcfR, cutoff = .95)
## 13 samples are above a 0.95 missing data cutoff, and were removed from VCF
#remove invariant sites generated by sample trimming
vcfR<-min_mac(vcfR, min.mac = 1)
## 55.03% of SNPs fell below a minor allele count of 1 and were removed from the VCF
### interrogate potential batch effects between runs
#interrogate batch effects between runs
#make a popmap where pop corresponds to the run the sample was on
batch.map<-sample.info[sample.info$id %in% colnames(vcfR@gt)[-1],c(1,2)]
colnames(batch.map)<-c("id","pop")
batch.map$pop<-as.factor(batch.map$pop)
#
assess_missing_data_pca(vcfR, popmap=batch.map, thresholds = .8, clustering = FALSE)
## cutoff is specified, filtered vcfR object will be returned
## 88.99% of SNPs fell below a completeness cutoff of 0.8 and were removed from the VCF
## [[1]]
## PC1 PC2 PC3 PC4
## T_albicilla_22581 -5.619609845 -9.82423507 -5.6631683 2.3753143742
## T_albicilla_22591 -5.717423623 -9.88407832 -5.7154664 2.2913904378
## T_albicilla_22592 -5.725967485 -9.80079329 -5.6737443 2.2766582539
## T_albicilla_22611 -4.177796800 -6.52279651 -3.9054526 1.5877132656
## T_albicilla_85104 -5.708193812 -9.87950482 -5.7359311 2.2453156553
## T_albicilla_85105 -5.661645281 -9.63322160 -5.5898141 2.2380803530
## T_chloris_12584 -2.884902571 -2.61955068 8.1764285 -5.4891731231
## T_chloris_12606 -2.896752624 -2.71588726 7.4748149 -5.6826017864
## T_chloris_13960 -2.716946308 -3.01561267 7.8290716 -8.3586270427
## T_chloris_14446 -2.736092002 -2.67819100 7.7600161 -7.9962968064
## T_chloris_20983 -2.752570486 -2.74826379 8.1036382 -8.0475199804
## T_chloris_22075 -3.006894426 -2.71251205 8.6099593 -5.6564391268
## T_chloris_23253 -2.907370296 -2.80075499 7.5707122 -4.9613340778
## T_chloris_23630 -2.856405177 -3.26997231 6.0917551 -7.8209230467
## T_chloris_23631 -1.461939224 -1.63024908 2.3286337 -3.1018058614
## T_chloris_23632 -2.854743492 -3.12448942 6.1080070 -7.5652742772
## T_chloris_24382 -2.741577175 -2.39812786 7.5527231 -5.2691158023
## T_chloris_24727 -2.730142432 -2.21793363 7.9485378 -4.8469893655
## T_chloris_67535_run1 -1.183571360 -0.65104200 2.1914300 -1.7665941618
## T_colonus_2003089 -3.236104984 -4.24886839 -0.1985283 -1.2274368611
## T_colonus_2003097 -3.252622113 -3.89149866 0.1863762 -1.7455248434
## T_colonus_2004070 -3.347047335 -4.33957576 -0.7487441 -2.0217012839
## T_leucopygius_32019 32.156637096 -7.68813066 -0.5236433 -0.0262991803
## T_leucopygius_32037 23.579958015 -5.75422262 -0.1235100 -0.2374579633
## T_leucopygius_34505 33.394251349 -7.82399769 -0.7054102 -0.0107270786
## T_leucopygius_34508 25.452165860 -6.40525065 -0.1552226 -0.3842523452
## T_leucopygius_DOT6654 31.315823162 -7.58135803 -0.5802596 0.0453003289
## T_sanctus_14877 0.144250151 7.01000299 -1.8642038 -0.2064376433
## T_sanctus_14879 -0.105022825 4.70947603 -1.3541403 -0.4080206729
## T_sanctus_24565 -0.058257699 7.30848609 -2.2670582 -0.0421039302
## T_sanctus_25117 0.275331255 6.68863347 -2.2125103 -0.1415831628
## T_sanctus_33267 0.269760832 7.37325536 -2.0721071 -0.0805246535
## T_sanctus_34636 0.257242492 7.86456970 -2.0315766 -0.6460816853
## T_sanctus_34659 -0.001213983 5.38260853 -1.5678394 0.3210876173
## T_sanctus_35549 0.143420240 6.49109106 -1.5351844 -0.1935377864
## T_sanctus_72545 0.166613468 6.95411287 -2.0090657 -0.0345705931
## T_sanctus_7567 0.209542062 7.69085141 -1.6149440 -0.1383699437
## T_sanctus_76296 -0.439995574 2.80075239 -0.5693844 -0.0009532665
## T_sanctus_B29435 0.021065569 6.52533731 -2.8007788 -0.5141668348
## T_sanctus_B32637 0.369714208 5.73534094 -1.5789716 -0.2771985148
## T_sanctus_B33280 0.414484926 7.25632583 -2.7907777 -0.4252982667
## T_sanctus_B34636 0.332471701 7.94210474 -2.1278755 -0.3392297193
## T_sanctus_B34659 0.660989994 7.99482034 -2.7835523 0.3155432926
## T_sanctus_B34946 0.195439801 7.27462921 -2.2758726 -0.3893582838
## T_sanctus_B43266 0.372644203 6.81233830 -2.2627966 0.1003798172
## T_sanctus_B50292 0.545072524 7.84750287 -2.3215220 0.1300588197
## T_sanctus_B50543 0.536775932 7.32920111 -2.5935509 -0.2584869904
## T_sanctus_B51072 0.273104652 7.37796029 -2.6418314 0.1314908067
## T_sanctus_B52989 0.164156664 3.91121780 -0.9070095 -0.3531468615
## T_sanctus_B53055 0.239746477 5.46171490 -1.6976754 0.1237263016
## T_sanctus_B53068 0.409551444 6.67313187 -1.7470300 -0.4709559068
## T_sanctus_B54673 0.145915084 7.31614939 -2.1007063 0.1242138379
## T_sanctus_B57402 0.406664600 6.50264593 -2.2997550 0.1292246397
## T_sanctus_B59372 0.276809468 7.33980547 -2.0514218 -0.0633623618
## T_sanctus_B60180 0.338370604 6.28172415 -2.0701641 -1.1810266008
## T_sanctus_B60181 0.515601356 7.80712980 -2.6216591 -0.3509515877
## T_sanctus_B60182 0.486913169 8.11988494 -2.2452738 0.0097850298
## T_sanctus_B60183 0.006026180 7.74815281 -2.5653264 -0.0683995764
## T_sanctus_B60184 0.372657771 8.48364907 -1.6589288 0.0758657577
## T_saurophagus_18929 -5.563403753 -9.63334822 -6.1244247 1.5574980378
## T_saurophagus_27804 -5.601051937 -9.62802681 -5.7903054 1.6476538340
## T_saurophagus_36179 -5.666060279 -9.95887314 -6.4454691 1.8148574239
## T_saurophagus_36283 -4.299852715 -7.87587918 -4.5328983 0.9515986165
## T_saurophagus_36284 -5.589355434 -9.76792204 -6.3393952 1.8041122463
## T_saurophagus_69666 -3.508363950 -5.66719078 -3.3335593 1.1405430604
## T_sordidus_B33717 -1.456349993 0.13617120 10.6417458 9.3865758073
## T_sordidus_B33718 -1.685771966 -0.03722172 10.5812971 8.9649628491
## T_sordidus_B33719 -1.395525575 0.05947083 9.4973363 8.8314406330
## T_sordidus_B33720 -1.149771876 0.25129289 9.2180778 8.5617732892
## T_sordidus_B44198 -1.529978048 -0.45861039 8.9517891 7.8208246186
## T_sordidus_B44295 -1.735515698 -0.56895009 8.8991997 8.0191337106
## T_sordidus_B44296 -1.476192151 -0.87763038 8.7500529 7.6275179921
## T_sordidus_B51462 -1.558207787 -0.19103853 9.7547024 8.9684620483
## T_tristrami_18953 -4.729052772 -7.66111196 -2.8790853 -0.3772306207
## T_tristrami_27723 -4.066837450 -6.99635502 -2.5383971 -0.2535373319
## T_tristrami_27752 -2.821682559 -5.22588119 -1.5838331 -0.5459367417
## T_tristrami_27792 -3.301542964 -5.21193993 -1.3370356 -0.5087129076
## T_tristrami_27793 -4.266958713 -6.73543498 -2.1798357 -0.2456332747
## T_tristrami_32049 -4.636546122 -7.36322135 -2.4202593 -0.6801370775
## T_tristrami_33253 -4.642341602 -7.36230901 -2.9006873 -0.1149905375
## T_tristrami_33839 0.462467250 7.35308849 -1.9572941 0.7809419349
## T_tristrami_33858 0.173492298 5.04864744 -1.2549830 0.0715561002
## T_tristrami_33864 0.249679458 7.38874575 -1.9840580 -0.7857049504
## T_tristrami_33867 0.535852411 7.42322819 -2.3030836 0.4258100168
## T_tristrami_33895 0.490705756 6.43634224 -1.8794549 -0.4896334902
## T_tristrami_36188 -4.135723647 -6.89745790 -2.6704629 -0.1070496166
## T_tristrami_6704 -4.764473559 -8.13307255 -3.2123944 0.0120145979
## PC5 pop missing
## T_albicilla_22581 -5.872573828 2 0.039509389
## T_albicilla_22591 -6.293191137 2 0.014219038
## T_albicilla_22592 -6.201250149 1 0.023119505
## T_albicilla_22611 -4.144467829 1 0.268425052
## T_albicilla_85104 -5.992700394 1 0.039400847
## T_albicilla_85105 -6.049712586 1 0.040377727
## T_chloris_12584 -1.135361618 1 0.008466298
## T_chloris_12606 -1.113174651 1 0.030283295
## T_chloris_13960 -2.181362549 1 0.024747639
## T_chloris_14446 -2.165722818 1 0.014978834
## T_chloris_20983 -2.316695124 1 0.016824053
## T_chloris_22075 -1.273559728 1 0.013567785
## T_chloris_23253 -1.115072761 1 0.059806795
## T_chloris_23630 -2.419407590 2 0.107891024
## T_chloris_23631 -0.974303777 1 0.543037013
## T_chloris_23632 -2.519934401 1 0.099641810
## T_chloris_24382 -1.449010952 1 0.072180614
## T_chloris_24727 -1.148200218 1 0.114620645
## T_chloris_67535_run1 -0.146057111 1 0.595897102
## T_colonus_2003089 4.292569904 1 0.109844785
## T_colonus_2003097 4.046463687 1 0.091066971
## T_colonus_2004070 4.700492860 1 0.110713123
## T_leucopygius_32019 -0.139754801 3 0.110278954
## T_leucopygius_32037 0.225811589 3 0.355367416
## T_leucopygius_34505 -0.356473578 3 0.094757408
## T_leucopygius_34508 0.153828882 3 0.297297297
## T_leucopygius_DOT6654 -0.306048834 3 0.146206447
## T_sanctus_14877 -0.460931802 1 0.036578747
## T_sanctus_14879 -0.231898620 1 0.320850971
## T_sanctus_24565 0.052571997 1 0.012807989
## T_sanctus_25117 0.011576109 1 0.073374579
## T_sanctus_33267 -0.302170056 1 0.022468251
## T_sanctus_34636 -0.637225767 1 0.019646152
## T_sanctus_34659 0.302937983 1 0.232280473
## T_sanctus_35549 0.139231811 1 0.073917291
## T_sanctus_72545 0.055748452 1 0.037664170
## T_sanctus_7567 0.043248927 1 0.022902420
## T_sanctus_76296 -0.099629939 1 0.477043308
## T_sanctus_B29435 -0.006436275 2 0.089764463
## T_sanctus_B32637 -0.102098696 2 0.268967763
## T_sanctus_B33280 -0.162668608 2 0.146206447
## T_sanctus_B34636 -0.579462141 2 0.029957669
## T_sanctus_B34659 0.255683907 2 0.040377727
## T_sanctus_B34946 -0.366631440 2 0.040377727
## T_sanctus_B43266 0.057328968 2 0.091392597
## T_sanctus_B50292 -0.253276174 2 0.079561489
## T_sanctus_B50543 0.118707875 2 0.018126560
## T_sanctus_B51072 0.171413815 2 0.013350700
## T_sanctus_B52989 -0.347880579 2 0.425811354
## T_sanctus_B53055 -0.444358656 2 0.243460328
## T_sanctus_B53068 -0.616644834 2 0.057418865
## T_sanctus_B54673 -0.558788075 2 0.037772712
## T_sanctus_B57402 -0.776929754 2 0.179963096
## T_sanctus_B59372 0.007531646 2 0.008574840
## T_sanctus_B60180 0.030839294 2 0.248453273
## T_sanctus_B60181 -0.042389851 2 0.080104201
## T_sanctus_B60182 0.155040704 2 0.010745685
## T_sanctus_B60183 -0.545305872 2 0.018235103
## T_sanctus_B60184 0.153601918 2 0.011722566
## T_saurophagus_18929 -2.878916587 1 0.018235103
## T_saurophagus_27804 -3.343678450 1 0.010420059
## T_saurophagus_36179 -3.286922258 2 0.013133616
## T_saurophagus_36283 -2.322460564 2 0.248019103
## T_saurophagus_36284 -3.213173648 2 0.006295452
## T_saurophagus_69666 -1.787985720 1 0.365244763
## T_sordidus_B33717 0.340856841 2 0.015630088
## T_sordidus_B33718 0.150296348 1 0.014653207
## T_sordidus_B33719 0.094791196 2 0.128839683
## T_sordidus_B33720 0.140565504 2 0.139910995
## T_sordidus_B44198 -0.020180007 2 0.124497992
## T_sordidus_B44295 0.259868209 1 0.058287203
## T_sordidus_B44296 0.081474251 2 0.155975252
## T_sordidus_B51462 -0.112640792 2 0.072723326
## T_tristrami_18953 7.978119685 1 0.023770759
## T_tristrami_27723 6.104783708 2 0.133507001
## T_tristrami_27752 4.858770144 2 0.378704005
## T_tristrami_27792 5.631588635 1 0.233474438
## T_tristrami_27793 7.055494182 1 0.052534462
## T_tristrami_32049 8.148850759 1 0.026701400
## T_tristrami_33253 8.646526214 1 0.007597959
## T_tristrami_33839 -0.379724289 2 0.018994899
## T_tristrami_33858 -0.396295021 2 0.275805926
## T_tristrami_33864 -0.170461442 2 0.015087377
## T_tristrami_33867 -0.129652402 2 0.017692391
## T_tristrami_33895 0.316046865 2 0.172690763
## T_tristrami_36188 7.399634991 2 0.123738196
## T_tristrami_6704 7.708556895 1 0.033431021
#samples are clustering as species and within species by missing data, no indication of batch effects here
#visualize missing data by SNP and the effect of various cutoffs on the missingness of each sample
missing_by_snp(vcfR)
## cutoff is not specified, exploratory visualizations will be generated
## Picking joint bandwidth of 0.0708
## filt missingness snps.retained
## 1 0.30 0.37867104 38368
## 2 0.50 0.26724679 25480
## 3 0.60 0.21218939 19571
## 4 0.65 0.18834898 17054
## 5 0.70 0.16464662 14578
## 6 0.75 0.13461192 11480
## 7 0.80 0.11262072 9213
## 8 0.85 0.08904051 6762
## 9 0.90 0.05966766 3747
## 10 0.95 0.03138883 1304
## 11 1.00 0.00000000 66
#still need to target specific samples with too much missing data even at high filtering thresholds, for removal
#rerun missing by sample
miss<-missing_by_sample(vcfR=vcfR)
## No popmap provided
#show me the samples with the most missing data at a 85% completeness threshold
filt<-miss[miss$filt == .8,]
filt[order(filt$snps.retained),]
## indiv filt snps.retained
## 280 T_chloris_67535_run1 0.8 3723
## 276 T_chloris_23631 0.8 4210
## 299 T_sanctus_76296 0.8 4818
## 310 T_sanctus_B52989 0.8 5290
## 337 T_tristrami_27752 0.8 5724
## 326 T_saurophagus_69666 0.8 5848
## 285 T_leucopygius_32037 0.8 5939
## 290 T_sanctus_14879 0.8 6257
## 287 T_leucopygius_34508 0.8 6474
## 343 T_tristrami_33858 0.8 6672
## 301 T_sanctus_B32637 0.8 6735
## 265 T_albicilla_22611 0.8 6740
## 316 T_sanctus_B60180 0.8 6924
## 324 T_saurophagus_36283 0.8 6928
## 311 T_sanctus_B53055 0.8 6970
## 338 T_tristrami_27792 0.8 7062
## 295 T_sanctus_34659 0.8 7073
## 314 T_sanctus_B57402 0.8 7555
## 346 T_tristrami_33895 0.8 7622
## 333 T_sordidus_B44296 0.8 7776
## 288 T_leucopygius_DOT6654 0.8 7866
## 302 T_sanctus_B33280 0.8 7866
## 330 T_sordidus_B33720 0.8 7924
## 336 T_tristrami_27723 0.8 7983
## 329 T_sordidus_B33719 0.8 8026
## 331 T_sordidus_B44198 0.8 8066
## 347 T_tristrami_36188 0.8 8073
## 279 T_chloris_24727 0.8 8157
## 283 T_colonus_2004070 0.8 8193
## 284 T_leucopygius_32019 0.8 8197
## 281 T_colonus_2003089 0.8 8201
## 275 T_chloris_23630 0.8 8219
## 277 T_chloris_23632 0.8 8295
## 286 T_leucopygius_34505 0.8 8340
## 306 T_sanctus_B43266 0.8 8371
## 282 T_colonus_2003097 0.8 8374
## 300 T_sanctus_B29435 0.8 8386
## 317 T_sanctus_B60181 0.8 8475
## 307 T_sanctus_B50292 0.8 8480
## 296 T_sanctus_35549 0.8 8532
## 292 T_sanctus_25117 0.8 8537
## 334 T_sordidus_B51462 0.8 8543
## 278 T_chloris_24382 0.8 8548
## 274 T_chloris_23253 0.8 8662
## 332 T_sordidus_B44295 0.8 8676
## 312 T_sanctus_B53068 0.8 8684
## 339 T_tristrami_27793 0.8 8729
## 267 T_albicilla_85105 0.8 8841
## 304 T_sanctus_B34659 0.8 8841
## 305 T_sanctus_B34946 0.8 8841
## 262 T_albicilla_22581 0.8 8849
## 266 T_albicilla_85104 0.8 8850
## 313 T_sanctus_B54673 0.8 8865
## 297 T_sanctus_72545 0.8 8866
## 289 T_sanctus_14877 0.8 8876
## 348 T_tristrami_6704 0.8 8905
## 269 T_chloris_12606 0.8 8934
## 303 T_sanctus_B34636 0.8 8937
## 340 T_tristrami_32049 0.8 8967
## 270 T_chloris_13960 0.8 8985
## 335 T_tristrami_18953 0.8 8994
## 264 T_albicilla_22592 0.8 9000
## 298 T_sanctus_7567 0.8 9002
## 293 T_sanctus_33267 0.8 9006
## 294 T_sanctus_34636 0.8 9032
## 342 T_tristrami_33839 0.8 9038
## 319 T_sanctus_B60183 0.8 9045
## 321 T_saurophagus_18929 0.8 9045
## 308 T_sanctus_B50543 0.8 9046
## 345 T_tristrami_33867 0.8 9050
## 272 T_chloris_20983 0.8 9058
## 327 T_sordidus_B33717 0.8 9069
## 344 T_tristrami_33864 0.8 9074
## 271 T_chloris_14446 0.8 9075
## 328 T_sordidus_B33718 0.8 9078
## 263 T_albicilla_22591 0.8 9082
## 273 T_chloris_22075 0.8 9088
## 309 T_sanctus_B51072 0.8 9090
## 323 T_saurophagus_36179 0.8 9092
## 291 T_sanctus_24565 0.8 9095
## 320 T_sanctus_B60184 0.8 9105
## 318 T_sanctus_B60182 0.8 9114
## 322 T_saurophagus_27804 0.8 9117
## 315 T_sanctus_B59372 0.8 9134
## 268 T_chloris_12584 0.8 9135
## 341 T_tristrami_33253 0.8 9143
## 325 T_saurophagus_36284 0.8 9155
#drop the three continuing outlier samples at a 85% SNP completeness threshold
vcfR<- vcfR[,colnames(vcfR@gt) != "T_chloris_67535_run1" &
colnames(vcfR@gt) != "T_chloris_23631" &
colnames(vcfR@gt) != "T_sanctus_76296" &
colnames(vcfR@gt) != "T_sanctus_B52989"]
#remove invariant SNPs
vcfR<-min_mac(vcfR, min.mac = 1)
## 3.47% of SNPs fell below a minor allele count of 1 and were removed from the VCF
vcfR
## ***** Object of Class vcfR *****
## 83 samples
## 194 CHROMs
## 80,776 variants
## Object size: 214.5 Mb
## 64.46 percent missing data
## ***** ***** *****
#re-visualize missing data by SNP and the effect of various cutoffs on the missingness of each sample
missing_by_snp(vcfR)
## cutoff is not specified, exploratory visualizations will be generated
## Picking joint bandwidth of 0.0683
## filt missingness snps.retained
## 1 0.30 0.37361219 39441
## 2 0.50 0.25707739 26163
## 3 0.60 0.20532767 20689
## 4 0.65 0.18083119 18133
## 5 0.70 0.14973052 14917
## 6 0.75 0.12481566 12377
## 7 0.80 0.10038540 9910
## 8 0.85 0.07571551 7430
## 9 0.90 0.05149154 5011
## 10 0.95 0.02791287 2636
## 11 1.00 0.00000000 300
#all samples look decent at high thresholds
#make popmap
popmap<-sample.info[sample.info$id %in% colnames(vcfR@gt)[-1],c(1,5)]
colnames(popmap)<-c("id","pop")
popmap$pop<-as.factor(popmap$pop)
#assess missing data effects on clustering
assess_missing_data_pca(vcfR = vcfR, popmap = popmap, thresholds = c(.75,.8,.85), clustering = FALSE)
## cutoff is specified, filtered vcfR object will be returned
## 84.68% of SNPs fell below a completeness cutoff of 0.75 and were removed from the VCF
## cutoff is specified, filtered vcfR object will be returned
## 87.73% of SNPs fell below a completeness cutoff of 0.8 and were removed from the VCF
## cutoff is specified, filtered vcfR object will be returned
## 90.8% of SNPs fell below a completeness cutoff of 0.85 and were removed from the VCF
## [[1]]
## PC1 PC2 PC3 PC4
## T_albicilla_22581 7.0121667 -11.0542908 -7.04969813 1.76177557
## T_albicilla_22591 7.3296157 -11.4351352 -7.32346820 1.85847022
## T_albicilla_22592 7.2348018 -11.1700446 -7.24323460 1.85246241
## T_albicilla_22611 5.1386906 -7.1723689 -4.81785836 1.40353643
## T_albicilla_85104 7.1254748 -10.8769395 -7.20980916 1.93330690
## T_albicilla_85105 7.0452229 -10.6757005 -6.98833498 1.92866178
## T_chloris_12584 4.1996443 -3.2481522 10.33987648 -6.38570656
## T_chloris_12606 3.9406958 -2.9281397 9.39164631 -6.66917818
## T_chloris_13960 3.8584281 -3.2334374 10.10877582 -9.42290305
## T_chloris_14446 3.9190017 -3.0409967 10.26880994 -9.12175722
## T_chloris_20983 3.9943601 -3.1548780 10.61499048 -9.12263727
## T_chloris_22075 4.1667635 -2.9617041 11.11217144 -6.65032619
## T_chloris_23253 3.7881375 -2.6992906 8.79958377 -5.56697016
## T_chloris_23630 3.5725535 -3.4315625 7.65171376 -7.74165518
## T_chloris_23632 3.9034378 -3.1958691 7.80865230 -7.72389003
## T_chloris_24382 3.6258084 -2.4778154 9.20699003 -6.30261635
## T_chloris_24727 3.6099238 -2.0625425 9.23297379 -5.41808640
## T_colonus_2003089 4.2576035 -4.2716136 0.05452408 -1.50333321
## T_colonus_2003097 4.1274821 -3.8523564 0.52533832 -1.76127104
## T_colonus_2004070 4.3872330 -4.4181938 -0.49481431 -2.10147416
## T_leucopygius_32019 -36.0984446 -10.9610646 -0.16264739 -0.34301185
## T_leucopygius_32037 -26.9886590 -8.0719500 0.21679712 -0.10753881
## T_leucopygius_34505 -37.6777214 -11.3757775 -0.22900681 -0.13009757
## T_leucopygius_34508 -28.8525385 -8.8433370 0.22757448 -0.47258652
## T_leucopygius_DOT6654 -35.2178405 -10.6458975 -0.24783081 -0.18743472
## T_sanctus_14877 -1.0189915 8.7750105 -2.31136481 -0.48397043
## T_sanctus_14879 -0.3966857 5.7087024 -1.37514512 -0.42178233
## T_sanctus_24565 -0.7403862 9.0319056 -2.73269358 -0.09900194
## T_sanctus_25117 -1.0037876 8.1538841 -2.32106467 -0.30825914
## T_sanctus_33267 -1.2352819 9.2364888 -2.39759861 -0.24571407
## T_sanctus_34636 -1.0026027 9.4172542 -2.51520808 -0.73129240
## T_sanctus_34659 -0.6532669 6.2523593 -1.51104271 0.26325900
## T_sanctus_35549 -0.7134587 7.6064671 -1.52748212 -0.44948412
## T_sanctus_72545 -0.7439014 8.4283878 -2.09711871 -0.30490331
## T_sanctus_7567 -0.9733815 9.1112542 -1.77959678 -0.34560827
## T_sanctus_B29435 -0.8748905 7.6783686 -2.71475844 -0.67520500
## T_sanctus_B32637 -0.9278681 6.1592727 -1.81590305 -0.32818595
## T_sanctus_B33280 -1.1366560 7.8913742 -2.70104518 -0.73747100
## T_sanctus_B34636 -1.0679826 9.2741254 -2.54336162 -0.43019430
## T_sanctus_B34659 -1.5171704 9.0087426 -3.28036161 0.02924152
## T_sanctus_B34946 -0.9303180 8.4874878 -2.30099439 -0.49666269
## T_sanctus_B43266 -0.9285970 7.5837405 -2.00258384 -0.16938556
## T_sanctus_B50292 -1.2446582 8.7264615 -2.58426202 0.01128691
## T_sanctus_B50543 -1.3810840 9.0736433 -3.09119936 -0.35788985
## T_sanctus_B51072 -1.1513129 8.9686316 -2.98727441 0.02972107
## T_sanctus_B53055 -0.6879519 5.7790918 -1.54661531 0.10431938
## T_sanctus_B53068 -1.0929738 7.9003911 -1.81822131 -0.53725489
## T_sanctus_B54673 -1.0327342 8.7533743 -2.37175274 -0.02151578
## T_sanctus_B57402 -1.0173929 6.9349038 -2.52868292 -0.09178685
## T_sanctus_B59372 -1.0430501 9.0809128 -2.50910701 -0.02139196
## T_sanctus_B60180 -0.9963268 6.8584212 -2.05663365 -1.28588228
## T_sanctus_B60181 -1.3582288 8.9361777 -2.54439385 -0.53112919
## T_sanctus_B60182 -1.2534007 9.6475167 -2.59761202 -0.19065148
## T_sanctus_B60183 -1.0176890 9.5823300 -2.93417989 -0.11884465
## T_sanctus_B60184 -1.3294372 10.1209940 -2.07810375 -0.05955343
## T_saurophagus_18929 7.2281086 -10.9098179 -7.46109373 1.00409292
## T_saurophagus_27804 7.2556589 -10.9250839 -7.10555919 1.15234095
## T_saurophagus_36179 7.2500499 -11.1966130 -7.78817532 1.28236450
## T_saurophagus_36283 4.9210242 -8.2600709 -5.08204344 0.38219205
## T_saurophagus_36284 7.3408384 -11.2655985 -7.75299084 1.24807181
## T_saurophagus_69666 4.5859862 -6.1436285 -3.95032627 0.95323619
## T_sordidus_B33717 2.4308976 -0.3574010 12.21204937 11.40416418
## T_sordidus_B33718 2.7135812 -0.5410739 11.76947083 11.04834654
## T_sordidus_B33719 2.0437040 -0.3728679 10.20051581 10.30936110
## T_sordidus_B33720 1.7606294 -0.2313845 9.57257426 10.10200976
## T_sordidus_B44198 2.1966048 -0.9117969 9.49920107 9.48311449
## T_sordidus_B44295 2.6154588 -1.0239365 9.57471312 9.64473976
## T_sordidus_B44296 2.0884795 -1.3383391 9.48026708 9.11609663
## T_sordidus_B51462 2.2855812 -0.5669639 10.19118574 10.87931271
## T_tristrami_18953 6.2914294 -8.4422248 -3.54263685 -0.32449540
## T_tristrami_27723 4.8349788 -7.1311052 -2.84121438 -0.44677527
## T_tristrami_27752 3.1781011 -5.1635096 -1.61197733 -0.60472586
## T_tristrami_27792 4.1754542 -5.4045458 -1.84282897 -0.52937686
## T_tristrami_27793 5.6018004 -7.2675229 -2.94909420 -0.17416183
## T_tristrami_32049 6.0872566 -8.1367206 -3.37177596 -0.56680938
## T_tristrami_33253 6.1795486 -8.2606669 -3.60049751 -0.14718975
## T_tristrami_33839 -1.2678297 8.8791525 -2.13036469 0.79961757
## T_tristrami_33858 -0.6110964 5.2662522 -1.42391134 -0.18530633
## T_tristrami_33864 -0.9786316 8.8575360 -2.59612022 -0.61507484
## T_tristrami_33867 -1.2432742 8.9285815 -2.79760735 0.60314561
## T_tristrami_33895 -1.1125745 7.0053857 -1.92210576 -0.36154634
## T_tristrami_36188 5.0516680 -7.3169378 -3.09902760 -0.32309989
## T_tristrami_6704 6.1661925 -8.6777152 -3.84898012 -0.13419089
## PC5 PC6 PC7 PC8
## T_albicilla_22581 -6.974209456 0.47557915 5.271767670 -4.871267198
## T_albicilla_22591 -7.439804837 0.33965724 5.275563711 -4.991129105
## T_albicilla_22592 -7.091362737 0.31384699 5.030229138 -4.790033906
## T_albicilla_22611 -4.507965860 0.34011826 3.836307094 -3.222900332
## T_albicilla_85104 -6.828484701 0.62837153 4.853771794 -3.993637062
## T_albicilla_85105 -6.880966999 0.54913464 4.877002823 -3.778448218
## T_chloris_12584 -1.615337405 -8.07473884 1.742439228 1.681234477
## T_chloris_12606 -1.559791878 -7.71762766 2.003367110 1.013225629
## T_chloris_13960 -2.140280850 8.24626850 -3.239752836 -2.434596008
## T_chloris_14446 -1.955476960 8.60966752 -3.490966758 -2.547877069
## T_chloris_20983 -2.249805511 8.21193975 -3.583149381 -2.746264759
## T_chloris_22075 -1.678574136 -7.85856998 1.427676722 1.424257741
## T_chloris_23253 -1.487966433 -7.07217561 1.712592440 1.358009482
## T_chloris_23630 -1.936352177 6.17126435 -2.927860012 -2.313578037
## T_chloris_23632 -2.193284591 6.09974144 -2.264857009 -2.034992481
## T_chloris_24382 -2.074950426 -8.26108158 2.131810539 1.661871518
## T_chloris_24727 -1.659291094 -8.07928652 1.809237216 1.366337465
## T_colonus_2003089 5.644245608 5.88093840 9.360861438 8.649461717
## T_colonus_2003097 5.382461580 5.85761416 9.059623626 8.699491313
## T_colonus_2004070 6.095712775 5.70210614 9.525439380 8.547828183
## T_leucopygius_32019 -0.122400996 -0.14787477 0.179067085 -0.027288792
## T_leucopygius_32037 0.218098969 0.36492252 -0.187055213 -0.492034495
## T_leucopygius_34505 -0.309476678 -0.21939178 0.278031292 0.303086909
## T_leucopygius_34508 0.294710206 -0.03820655 -0.311011248 -0.140900878
## T_leucopygius_DOT6654 -0.217097674 -0.14226868 0.114394503 0.288071568
## T_sanctus_14877 -0.504188466 -0.62042847 0.149599136 -0.120953266
## T_sanctus_14879 -0.261663345 -0.13068101 -0.376560186 0.314916148
## T_sanctus_24565 -0.046458884 0.07459296 -0.281177388 0.103281213
## T_sanctus_25117 -0.002890203 0.01178232 -0.390045502 0.401925453
## T_sanctus_33267 -0.449984703 -0.38712998 -0.001925164 -0.321173617
## T_sanctus_34636 -0.480214097 -0.06010353 0.670669123 -0.576807852
## T_sanctus_34659 0.065160647 0.35485713 -0.715376112 -0.082507059
## T_sanctus_35549 0.079846206 0.22428826 -0.463304646 -0.312843625
## T_sanctus_72545 0.198963983 0.31124328 -0.521408925 -0.502720948
## T_sanctus_7567 -0.313223738 -0.23040274 -0.162973137 -0.320062047
## T_sanctus_B29435 0.026845311 0.55153187 0.344218529 0.843419413
## T_sanctus_B32637 -0.448504196 -0.52886141 -0.009859801 0.019552303
## T_sanctus_B33280 -0.281910044 -0.16511347 -0.449527650 -0.611732864
## T_sanctus_B34636 -0.407504212 0.03613173 0.788453981 -0.405503728
## T_sanctus_B34659 -0.065463466 -0.01163201 -0.807757277 0.013726820
## T_sanctus_B34946 -0.351404874 -0.03018599 0.046067499 -0.379861082
## T_sanctus_B43266 0.048706787 -0.15337162 -0.497923736 0.444855022
## T_sanctus_B50292 -0.571741680 0.50055781 -0.636341333 -0.350799192
## T_sanctus_B50543 -0.053117871 -0.21142943 -0.458386035 0.042903893
## T_sanctus_B51072 0.041941388 0.05266011 0.587328964 -0.372740395
## T_sanctus_B53055 -0.492803373 -0.44759631 0.142000379 -0.135359458
## T_sanctus_B53068 -0.452906231 0.34557907 -1.030172279 -0.517170089
## T_sanctus_B54673 -0.599647058 0.28185079 -0.192729306 0.010769192
## T_sanctus_B57402 -0.861435022 0.06433312 -0.029523341 -0.456524451
## T_sanctus_B59372 0.338621678 -0.26223951 -1.445992904 -0.395736385
## T_sanctus_B60180 -0.175871262 -0.16534749 0.835797384 0.419357242
## T_sanctus_B60181 -0.404478268 -0.67001884 0.849140181 -0.384971942
## T_sanctus_B60182 -0.082777941 -0.37211787 0.288978300 0.132516336
## T_sanctus_B60183 -0.951129338 -0.56044299 0.712501069 -0.194828457
## T_sanctus_B60184 0.019217515 -0.36326401 -0.019615731 0.280199941
## T_saurophagus_18929 -3.458978224 -0.48579947 -6.713872965 6.720748592
## T_saurophagus_27804 -3.682462406 -0.48858985 -5.937245064 5.970456240
## T_saurophagus_36179 -3.777696352 -0.53209163 -6.814187280 6.757433169
## T_saurophagus_36283 -2.309036752 -0.41652129 -4.643458226 4.118826703
## T_saurophagus_36284 -3.898775567 -0.57689696 -6.639273584 6.613264973
## T_saurophagus_69666 -2.011394923 -0.17370221 -3.862742977 3.725787977
## T_sordidus_B33717 0.019705336 0.78409681 -0.610854570 0.176995063
## T_sordidus_B33718 -0.202323938 1.09856953 -0.990441284 0.111789521
## T_sordidus_B33719 0.022487243 0.55930818 -0.817762566 0.154216026
## T_sordidus_B33720 -0.216260445 -0.13739699 -0.590534924 0.214911034
## T_sordidus_B44198 0.065996838 1.21834939 0.158539810 -0.369897638
## T_sordidus_B44295 0.176167071 0.93200915 0.186181967 -0.395637432
## T_sordidus_B44296 -0.173238884 1.07649976 -0.148579866 -0.351299188
## T_sordidus_B51462 -0.391114399 0.32077596 -0.529004889 -0.160475490
## T_tristrami_18953 9.226168771 -1.53288090 -1.826591899 -3.232734336
## T_tristrami_27723 6.647924648 -1.29326237 -1.139394022 -2.649409239
## T_tristrami_27752 4.872910759 -1.04908717 -0.688799762 -1.363225975
## T_tristrami_27792 5.992636466 -0.44711550 0.352831469 -2.046957139
## T_tristrami_27793 7.790159661 -1.63664456 -0.875010298 -3.318660763
## T_tristrami_32049 9.649967824 -1.23907559 -1.552762539 -3.606579525
## T_tristrami_33253 10.327562319 -1.55535025 -1.952473389 -3.443176301
## T_tristrami_33839 -0.500343812 0.10630646 -1.066312892 -0.503730306
## T_tristrami_33858 -0.524608591 0.14730857 0.012545070 -0.009221095
## T_tristrami_33864 -0.212115185 -0.72595869 -0.160067984 -0.652726757
## T_tristrami_33867 -0.027162111 0.38570494 -0.185308282 0.503151098
## T_tristrami_33895 0.238406919 0.64124395 0.589103524 0.543462318
## T_tristrami_36188 8.031363953 -1.41995987 -1.399678685 -3.140151718
## T_tristrami_6704 9.051720799 -1.17882974 -1.563528337 -3.560213996
## PC9 PC10 pop missing
## T_albicilla_22581 -0.2003713363 0.29997485 albicilla 0.05865719
## T_albicilla_22591 -0.1640565007 0.28140272 albicilla 0.01769411
## T_albicilla_22592 -0.2807100996 0.27766683 albicilla 0.03805446
## T_albicilla_22611 0.2106154151 0.26241912 albicilla 0.29878000
## T_albicilla_85104 -0.2067801883 0.19515839 albicilla 0.05849560
## T_albicilla_85105 -0.1103777375 0.15845476 albicilla 0.06011150
## T_chloris_12584 0.2780921007 0.19694020 chloris 0.01413913
## T_chloris_12606 0.0451716103 0.28969596 chloris 0.04371011
## T_chloris_13960 -0.3546547301 -0.89845140 chloris 0.04257898
## T_chloris_14446 -0.4545858200 -0.39590621 chloris 0.02205704
## T_chloris_20983 -0.3069659936 -0.57081054 chloris 0.02238022
## T_chloris_22075 -0.0455745598 0.48731295 chloris 0.01591662
## T_chloris_23253 0.1216404714 0.59307337 chloris 0.11012362
## T_chloris_23630 0.2024514286 -0.07964462 chloris 0.17451725
## T_chloris_23632 0.3682890249 0.27665226 chloris 0.13565484
## T_chloris_24382 -0.0006162337 0.49643673 chloris 0.10527592
## T_chloris_24727 0.3190902678 0.33982414 chloris 0.15035954
## T_colonus_2003089 -0.2508650684 0.46740898 colonus 0.13840187
## T_colonus_2003097 0.1517822161 0.57708436 colonus 0.13775551
## T_colonus_2004070 0.0799190312 0.32125531 colonus 0.14009857
## T_leucopygius_32019 0.0395610553 0.07604338 leucopygius 0.13226145
## T_leucopygius_32037 -0.0399074733 -0.29057141 leucopygius 0.36818292
## T_leucopygius_34505 -0.0804982134 0.26214961 leucopygius 0.11222429
## T_leucopygius_34508 -0.3892514531 -0.85743491 leucopygius 0.31671649
## T_leucopygius_DOT6654 0.5944954740 0.20798953 leucopygius 0.17168942
## T_sanctus_14877 -4.8834503659 -6.23255390 sanctus 0.05582936
## T_sanctus_14879 -1.8693697155 -1.91893545 sanctus 0.34442918
## T_sanctus_24565 1.0616152540 1.40023305 sanctus 0.02197625
## T_sanctus_25117 1.1358630712 0.81916206 sanctus 0.09267189
## T_sanctus_33267 0.2785348386 1.53282452 sanctus 0.03175244
## T_sanctus_34636 14.2671174865 -6.00670556 sanctus 0.03506504
## T_sanctus_34659 -0.9113232729 4.58440724 sanctus 0.26638119
## T_sanctus_35549 0.8871769683 1.16737732 sanctus 0.11133554
## T_sanctus_72545 -0.5512637421 1.31217989 sanctus 0.05534459
## T_sanctus_7567 -0.9343093908 3.10327462 sanctus 0.03902400
## T_sanctus_B29435 -0.2363037405 0.91096815 sanctus 0.14696615
## T_sanctus_B32637 -0.7253746413 1.75669068 sanctus 0.34539872
## T_sanctus_B33280 -0.4354222409 3.48235453 sanctus 0.22178234
## T_sanctus_B34636 14.0743092953 -5.65615374 sanctus 0.05833401
## T_sanctus_B34659 -0.9399070112 6.73862493 sanctus 0.07360427
## T_sanctus_B34946 1.2649495237 1.02179730 sanctus 0.07045326
## T_sanctus_B43266 -0.8204736989 1.49868467 sanctus 0.14664297
## T_sanctus_B50292 -0.5616866900 4.27131006 sanctus 0.12902965
## T_sanctus_B50543 0.0344275234 2.12697711 sanctus 0.02092591
## T_sanctus_B51072 -0.7494517090 1.63222564 sanctus 0.02221863
## T_sanctus_B53055 0.6574821479 0.84106042 sanctus 0.31607013
## T_sanctus_B53068 0.7893978559 2.43561026 sanctus 0.08855135
## T_sanctus_B54673 -0.0739832809 2.04908235 sanctus 0.07408904
## T_sanctus_B57402 -0.2483205042 1.57331901 sanctus 0.25143411
## T_sanctus_B59372 0.1568147308 2.01866721 sanctus 0.01413913
## T_sanctus_B60180 -2.7281457659 -4.23101791 sanctus 0.32705825
## T_sanctus_B60181 -4.5021158621 -6.05988781 sanctus 0.13169589
## T_sanctus_B60182 -3.4365229504 -7.20617141 sanctus 0.01583582
## T_sanctus_B60183 -5.4242838983 -8.34937473 sanctus 0.02763190
## T_sanctus_B60184 -5.3788043730 -6.92986257 sanctus 0.01672457
## T_saurophagus_18929 0.2034109133 -0.35435197 saurophagus 0.03716571
## T_saurophagus_27804 0.3172567005 -0.52659399 saurophagus 0.02431930
## T_saurophagus_36179 0.2658898175 -0.50946618 saurophagus 0.02682395
## T_saurophagus_36283 0.0815378888 -0.40752972 saurophagus 0.32180658
## T_saurophagus_36284 0.2323698839 -0.52562086 saurophagus 0.01123051
## T_saurophagus_69666 0.0977589240 -0.25785324 saurophagus 0.37852468
## T_sordidus_B33717 -0.0542296397 -0.43418304 sordidus 0.02730872
## T_sordidus_B33718 0.1721330922 0.14322501 sordidus 0.02286499
## T_sordidus_B33719 0.6542731642 -0.52912886 sordidus 0.19229215
## T_sordidus_B33720 0.4548270865 -0.64597532 sordidus 0.20255312
## T_sordidus_B44198 0.1101022682 0.14736387 sordidus 0.18712127
## T_sordidus_B44295 -0.5240656865 0.22372566 sordidus 0.09412620
## T_sordidus_B44296 -0.2630655306 -0.11568020 sordidus 0.22008564
## T_sordidus_B51462 -0.1771055517 -0.13174051 sordidus 0.11691040
## T_tristrami_18953 0.0467837275 -0.23211872 tristrami 0.04080149
## T_tristrami_27723 0.1189185718 -0.17116028 tristrami 0.19544316
## T_tristrami_27752 0.2674676879 -0.08680509 tristrami 0.45810778
## T_tristrami_27792 -0.3654840987 -0.50074421 tristrami 0.29708330
## T_tristrami_27793 -0.3091475000 -0.15545798 tristrami 0.09008645
## T_tristrami_32049 0.5083792115 0.22514162 tristrami 0.03967036
## T_tristrami_33253 -0.0808743448 -0.16771567 tristrami 0.01203846
## T_tristrami_33839 1.0237599502 1.78936200 tristrami 0.03417629
## T_tristrami_33858 -0.8905985696 0.93067931 tristrami 0.35283187
## T_tristrami_33864 -0.6428311767 2.68466676 tristrami 0.02092591
## T_tristrami_33867 -0.2194380943 2.51237180 tristrami 0.02965177
## T_tristrami_33895 0.3739009477 1.32236686 tristrami 0.24715198
## T_tristrami_36188 0.2228433099 -0.45530682 tristrami 0.17847621
## T_tristrami_6704 -0.3478414825 -0.43176253 tristrami 0.06188899
##
## [[2]]
## PC1 PC2 PC3 PC4
## T_albicilla_22581 6.092947696 -10.072082827 -5.955672604 2.38848790
## T_albicilla_22591 6.220846982 -10.164918610 -5.995341116 2.30394461
## T_albicilla_22592 6.205398580 -10.066810857 -5.907150214 2.28911882
## T_albicilla_22611 4.440754567 -6.492130635 -3.963400516 1.54476154
## T_albicilla_85104 6.172358440 -10.066497872 -5.915553310 2.30328175
## T_albicilla_85105 6.109579562 -9.795865850 -5.831407772 2.33362104
## T_chloris_12584 3.230539703 -2.695106240 8.625426954 -5.94335385
## T_chloris_12606 3.142689903 -2.545845234 7.859712981 -6.27507146
## T_chloris_13960 3.035768301 -3.031292928 8.194600204 -8.92521330
## T_chloris_14446 3.061330574 -2.685705526 8.296823078 -8.59335736
## T_chloris_20983 3.098933715 -2.718770393 8.725212630 -8.66144046
## T_chloris_22075 3.291518911 -2.621846442 9.103738068 -6.17076720
## T_chloris_23253 3.082581783 -2.546130203 7.700124510 -5.38955177
## T_chloris_23630 3.101882443 -3.232118976 6.317223794 -7.95647414
## T_chloris_23632 3.069000344 -3.031121716 6.314523671 -7.79416245
## T_chloris_24382 2.901761931 -2.204895201 7.782230794 -5.83967492
## T_chloris_24727 2.921185491 -2.033089433 8.001002891 -5.27277329
## T_colonus_2003089 3.456613287 -4.144649375 -0.233417105 -1.37180859
## T_colonus_2003097 3.462898459 -3.804279239 0.185419338 -1.76115422
## T_colonus_2004070 3.597268806 -4.419759990 -0.741049927 -2.04163632
## T_leucopygius_32019 -32.967578551 -8.677047697 -0.423972137 -0.08124960
## T_leucopygius_32037 -23.892628848 -6.359954685 0.006619215 -0.22829750
## T_leucopygius_34505 -34.275036734 -8.877413289 -0.574109545 -0.02606897
## T_leucopygius_34508 -26.050806383 -7.220040359 -0.102190186 -0.43485895
## T_leucopygius_DOT6654 -32.050581053 -8.492931925 -0.478400373 -0.05869077
## T_sanctus_14877 -0.369307461 7.433510144 -1.981294403 -0.21007325
## T_sanctus_14879 -0.001792175 4.863881249 -1.294683592 -0.37802636
## T_sanctus_24565 -0.119730890 7.760456735 -2.472513231 -0.05545290
## T_sanctus_25117 -0.525087704 7.210789913 -2.232622386 -0.13326772
## T_sanctus_33267 -0.560090453 7.926831761 -2.185049308 -0.09418472
## T_sanctus_34636 -0.455528476 8.300712876 -2.035397363 -0.79828856
## T_sanctus_34659 -0.085473957 5.539518329 -1.496671401 0.27774286
## T_sanctus_35549 -0.349372104 6.830507783 -1.474377748 -0.26433323
## T_sanctus_72545 -0.334070083 7.225620782 -1.928113392 -0.13126942
## T_sanctus_7567 -0.413790790 8.017743239 -1.635983210 -0.23995738
## T_sanctus_B29435 -0.272230971 6.870347595 -2.792770429 -0.42362772
## T_sanctus_B32637 -0.582569627 6.063104091 -1.788794347 -0.27244556
## T_sanctus_B33280 -0.720847551 7.707582185 -2.903556447 -0.29837177
## T_sanctus_B34636 -0.518050241 8.314336391 -2.171000719 -0.44066968
## T_sanctus_B34659 -0.873178875 8.365504803 -2.985199271 0.33168370
## T_sanctus_B34946 -0.371387960 7.433289384 -2.388533633 -0.18485581
## T_sanctus_B43266 -0.587459750 7.127769015 -2.249127304 0.01933968
## T_sanctus_B50292 -0.735782256 8.104274163 -2.323412713 0.32488903
## T_sanctus_B50543 -0.745892033 7.784955042 -2.682691025 -0.37450259
## T_sanctus_B51072 -0.486771124 7.792610873 -2.711690390 0.12628164
## T_sanctus_B53055 -0.365481495 5.609552765 -1.737803804 0.13685896
## T_sanctus_B53068 -0.599289708 7.020652304 -1.882806275 -0.47386086
## T_sanctus_B54673 -0.425965671 7.820207754 -2.223981319 0.03582019
## T_sanctus_B57402 -0.581305750 6.711352582 -2.373977292 0.16956998
## T_sanctus_B59372 -0.508711070 7.745063631 -2.018251380 -0.16938789
## T_sanctus_B60180 -0.592156473 6.571230042 -2.096035658 -1.22488965
## T_sanctus_B60181 -0.749659967 8.191265116 -2.576617125 -0.29578770
## T_sanctus_B60182 -0.699830922 8.483392786 -2.379503234 0.02888877
## T_sanctus_B60183 -0.267590419 8.228949949 -2.661716968 -0.06147706
## T_sanctus_B60184 -0.616697779 8.842604362 -1.719872193 -0.03534484
## T_saurophagus_18929 6.046950695 -9.860352523 -6.337639804 1.39873909
## T_saurophagus_27804 6.084444783 -9.917360528 -6.023092278 1.53425991
## T_saurophagus_36179 6.153311020 -10.166078589 -6.655676298 1.64627183
## T_saurophagus_36283 4.653765564 -8.066550258 -4.764132979 0.87080513
## T_saurophagus_36284 6.108329355 -10.044485206 -6.578631808 1.64862526
## T_saurophagus_69666 3.778596643 -5.689075096 -3.389871922 1.07990258
## T_sordidus_B33717 1.710584209 0.007376488 11.301956529 9.62029290
## T_sordidus_B33718 1.960771478 -0.186633023 11.195432854 9.26310280
## T_sordidus_B33719 1.591110360 -0.075682701 10.146295302 8.89320812
## T_sordidus_B33720 1.359780933 0.115049937 9.758664811 8.72742632
## T_sordidus_B44198 1.764694112 -0.567649821 9.553593498 7.97497298
## T_sordidus_B44295 1.961721835 -0.666418941 9.354633313 8.16554984
## T_sordidus_B44296 1.697766866 -0.954688141 9.306748401 7.76920150
## T_sordidus_B51462 1.825043052 -0.311243345 10.341448464 9.26415049
## T_tristrami_18953 5.165352673 -7.886499732 -2.999345747 -0.36478029
## T_tristrami_27723 4.410387948 -7.099961957 -2.635239677 -0.35657664
## T_tristrami_27752 3.046458866 -5.304486556 -1.646404905 -0.59487589
## T_tristrami_27792 3.482730954 -5.210578704 -1.528196339 -0.55670766
## T_tristrami_27793 4.614354064 -6.925410336 -2.368579825 -0.29720527
## T_tristrami_32049 5.037225767 -7.584817214 -2.526045769 -0.67842502
## T_tristrami_33253 5.032052514 -7.639138251 -3.021346776 -0.26461246
## T_tristrami_33839 -0.743700965 7.854736856 -1.970162095 0.80487127
## T_tristrami_33858 -0.333295744 5.245240109 -1.436376007 0.06680060
## T_tristrami_33864 -0.539337525 7.875852136 -2.317173630 -0.73369557
## T_tristrami_33867 -0.773127314 7.907570238 -2.453380649 0.46959678
## T_tristrami_33895 -0.678606957 6.722501307 -1.790068637 -0.34217194
## T_tristrami_36188 4.467389684 -7.120125556 -2.806638175 -0.14495414
## T_tristrami_6704 5.171120959 -8.348402734 -3.297715612 -0.09238323
## PC5 PC6 PC7 PC8
## T_albicilla_22581 -6.298258306 0.62767667 5.766140254 3.1522279346
## T_albicilla_22591 -6.661436001 0.52057293 5.720592539 3.0148091100
## T_albicilla_22592 -6.530661360 0.51032944 5.387559140 2.7968230699
## T_albicilla_22611 -4.161097444 0.49808556 3.848194835 1.7914694594
## T_albicilla_85104 -6.418281615 0.73243799 5.212044240 2.2921457041
## T_albicilla_85105 -6.367335627 0.63730359 5.177882620 2.1030001686
## T_chloris_12584 -1.346260145 -7.44350309 1.429590297 -1.8471395455
## T_chloris_12606 -1.372209202 -7.01624354 2.016043671 -1.3414731624
## T_chloris_13960 -2.291606717 7.11573717 -2.545291915 2.9115131827
## T_chloris_14446 -2.238240611 7.48317644 -2.439468281 2.8539150708
## T_chloris_20983 -2.413355742 6.91642292 -2.567757845 3.0885926620
## T_chloris_22075 -1.395107149 -6.92663668 1.184460449 -1.4387477513
## T_chloris_23253 -1.280449810 -6.36062656 1.377723238 -1.5211220400
## T_chloris_23630 -2.105815436 5.64335992 -2.444800087 2.5127372704
## T_chloris_23632 -2.335990895 5.38756884 -1.988529781 2.2928868305
## T_chloris_24382 -1.672960267 -7.46823986 1.647887946 -1.9049276810
## T_chloris_24727 -1.369090078 -7.32494118 1.760088241 -1.8398583967
## T_colonus_2003089 4.556137144 5.65844907 5.446864540 -9.8905595009
## T_colonus_2003097 4.376180023 5.67363585 5.208693125 -9.8786542790
## T_colonus_2004070 4.940357997 5.44277126 5.523089740 -9.8266482126
## T_leucopygius_32019 -0.208979823 -0.19608752 0.152323299 0.0237044028
## T_leucopygius_32037 0.191822272 0.31759262 -0.022057316 0.4342300366
## T_leucopygius_34505 -0.340673326 -0.23389526 0.156378911 -0.2538666268
## T_leucopygius_34508 0.130415173 -0.01620895 -0.121464077 0.0971132603
## T_leucopygius_DOT6654 -0.340733171 -0.09156867 -0.024493439 -0.1456255208
## T_sanctus_14877 -0.396073291 -0.45865761 0.494609458 0.0046867983
## T_sanctus_14879 -0.384883093 -0.02661100 -0.078237746 -0.2640684134
## T_sanctus_24565 0.079146832 -0.44774355 -0.451492043 0.1746052842
## T_sanctus_25117 0.044740188 -0.11856254 -0.517228503 -0.3446927897
## T_sanctus_33267 -0.341914436 -0.39864399 0.283247174 0.1389867818
## T_sanctus_34636 -0.668575504 -0.33533261 -0.024207452 0.5754392783
## T_sanctus_34659 0.223679726 0.30296760 -0.582525565 0.1556119538
## T_sanctus_35549 0.174653357 0.26327997 -0.189689627 0.0839633301
## T_sanctus_72545 0.088661056 0.24662732 -0.095743233 0.3489033770
## T_sanctus_7567 -0.094328440 -0.29175827 0.183806498 0.0887991455
## T_sanctus_B29435 0.072382414 0.46654923 -0.008587424 -0.5024098800
## T_sanctus_B32637 -0.219119065 -0.46086263 -0.003509084 0.0319698111
## T_sanctus_B33280 -0.157095801 -0.21437787 -0.332960078 0.6449317490
## T_sanctus_B34636 -0.586933315 -0.20701998 -0.000329519 0.5172166964
## T_sanctus_B34659 0.131030234 -0.20565258 -0.723215127 0.1459195176
## T_sanctus_B34946 -0.430753989 -0.25362266 -0.102314511 0.5957843893
## T_sanctus_B43266 0.151248600 -0.31561906 -0.108762223 -0.2422098124
## T_sanctus_B50292 -0.279941189 0.26987841 -0.447423484 0.5901838003
## T_sanctus_B50543 0.131909887 0.01359181 -0.325014885 -0.0888047842
## T_sanctus_B51072 0.149518824 0.22766399 0.714767168 0.1242419951
## T_sanctus_B53055 -0.438741474 -0.45650230 -0.026417158 0.3900021051
## T_sanctus_B53068 -0.482478460 0.22148353 -0.646424462 0.4023573925
## T_sanctus_B54673 -0.666217247 0.27873101 -0.281325787 -0.0552076031
## T_sanctus_B57402 -0.751204434 0.01373909 -0.236577881 0.5704562142
## T_sanctus_B59372 0.081713228 -0.31080489 -0.932551951 0.5477837722
## T_sanctus_B60180 -0.047354638 0.07012784 0.793931136 -0.4222468465
## T_sanctus_B60181 -0.209883057 -0.31835588 1.203855505 0.3992346960
## T_sanctus_B60182 0.091657079 -0.05905250 0.450250745 0.0009571224
## T_sanctus_B60183 -0.722978879 -0.21903947 0.846841083 -0.1934094065
## T_sanctus_B60184 0.165353303 -0.28421931 0.320185940 -0.2418419519
## T_saurophagus_18929 -2.954752435 -1.03336483 -7.482485044 -3.9973953511
## T_saurophagus_27804 -3.429289348 -1.00428040 -6.415912920 -3.5290916896
## T_saurophagus_36179 -3.355925085 -1.13790366 -7.540127253 -3.9140481492
## T_saurophagus_36283 -2.362801891 -0.84872019 -5.540059078 -2.6751985654
## T_saurophagus_36284 -3.332368002 -1.12638149 -7.342750750 -3.9642260666
## T_saurophagus_69666 -1.834807231 -0.59304316 -4.163051588 -2.0857800849
## T_sordidus_B33717 0.308450293 0.90065654 -0.467984537 0.0437621241
## T_sordidus_B33718 0.081083467 1.00244511 -0.989100600 0.1593810135
## T_sordidus_B33719 0.235714149 0.71952140 -0.866781567 -0.0333681844
## T_sordidus_B33720 0.101320778 -0.04270858 -0.835610426 -0.0940463399
## T_sordidus_B44198 0.007538713 1.17926063 0.197368280 0.2364324374
## T_sordidus_B44295 0.321157083 0.87501393 0.088792257 0.3402984846
## T_sordidus_B44296 -0.020835406 1.17018778 -0.106203915 0.3222657509
## T_sordidus_B51462 -0.171040247 0.27776856 -0.448898214 0.2738691827
## T_tristrami_18953 8.354048085 -1.08669113 -0.350613223 3.2701609773
## T_tristrami_27723 6.192153869 -1.06603337 -0.073821133 2.5628683585
## T_tristrami_27752 4.817998136 -1.04677148 -0.130292010 1.3850350699
## T_tristrami_27792 5.633309713 -0.33031051 0.817809323 1.6711763103
## T_tristrami_27793 7.199773895 -1.37875999 0.207708852 3.0424744034
## T_tristrami_32049 8.409930972 -0.67057013 -0.573285812 3.3109044403
## T_tristrami_33253 9.136560018 -1.15187021 -0.552318447 3.3272553021
## T_tristrami_33839 -0.420893960 0.09765055 -1.048826045 0.6470038549
## T_tristrami_33858 -0.317156551 0.28541825 -0.069643615 0.1839284256
## T_tristrami_33864 -0.270017088 -0.63525205 0.133391690 0.5797574521
## T_tristrami_33867 -0.025638437 0.45603646 -0.310440815 -0.6545402410
## T_tristrami_33895 0.351581509 0.71497501 0.233066440 -0.4798081973
## T_tristrami_36188 7.555056623 -1.04837374 -0.180029405 3.0483033291
## T_tristrami_6704 8.036260078 -0.55726935 -0.228551752 3.3689367841
## PC9 PC10 pop missing
## T_albicilla_22581 -0.052900091 0.322741756 albicilla 0.039455096
## T_albicilla_22591 -0.084307455 0.366213644 albicilla 0.014631685
## T_albicilla_22592 -0.015858408 0.304133631 albicilla 0.026841574
## T_albicilla_22611 -0.394697282 0.240497899 albicilla 0.284157417
## T_albicilla_85104 0.001673160 0.251239927 albicilla 0.048234107
## T_albicilla_85105 -0.106227942 0.330398468 albicilla 0.047830474
## T_chloris_12584 -0.223552668 0.269403805 chloris 0.009788093
## T_chloris_12606 0.111351513 0.210269782 chloris 0.037336024
## T_chloris_13960 0.354942817 -0.565684390 chloris 0.029061554
## T_chloris_14446 0.377229416 -0.041821008 chloris 0.015842583
## T_chloris_20983 0.352591311 -0.339831921 chloris 0.018567104
## T_chloris_22075 0.139492276 0.513491279 chloris 0.015035318
## T_chloris_23253 0.106396714 0.475215290 chloris 0.076387487
## T_chloris_23630 0.037286129 0.001475619 chloris 0.118668012
## T_chloris_23632 -0.131027033 0.104445175 chloris 0.118970737
## T_chloris_24382 0.017087988 0.360150382 chloris 0.089404642
## T_chloris_24727 -0.091584083 0.211530394 chloris 0.134207871
## T_colonus_2003089 -0.466510729 0.422280140 colonus 0.122603431
## T_colonus_2003097 -0.637862462 0.371211622 colonus 0.105449041
## T_colonus_2004070 -0.565934853 0.322423118 colonus 0.124924319
## T_leucopygius_32019 -0.173963753 0.081663736 leucopygius 0.117356206
## T_leucopygius_32037 0.334326700 -0.471519637 leucopygius 0.369323915
## T_leucopygius_34505 -0.003790306 0.318310947 leucopygius 0.101715439
## T_leucopygius_34508 0.577603668 -0.648716308 leucopygius 0.306659939
## T_leucopygius_DOT6654 -0.688769854 0.183155475 leucopygius 0.157013118
## T_sanctus_14877 4.017362746 -5.461522584 sanctus 0.043995964
## T_sanctus_14879 1.204709714 -1.284191667 sanctus 0.339051463
## T_sanctus_24565 -1.024012997 1.094588148 sanctus 0.015136226
## T_sanctus_25117 -1.076606255 0.510553040 sanctus 0.082038345
## T_sanctus_33267 -0.476017154 1.650413223 sanctus 0.026135217
## T_sanctus_34636 -12.589934563 -5.274328850 sanctus 0.025428860
## T_sanctus_34659 1.154880365 3.794758780 sanctus 0.248839556
## T_sanctus_35549 -1.025439805 1.216998130 sanctus 0.087991927
## T_sanctus_72545 0.441631446 0.970165121 sanctus 0.045408678
## T_sanctus_7567 0.271301414 2.579273716 sanctus 0.028456105
## T_sanctus_B29435 0.021439598 0.433001189 sanctus 0.097578204
## T_sanctus_B32637 0.662512715 1.723735002 sanctus 0.281130172
## T_sanctus_B33280 0.134988621 3.618571520 sanctus 0.153077699
## T_sanctus_B34636 -12.482978590 -5.147555782 sanctus 0.033905146
## T_sanctus_B34659 1.480150901 5.577428634 sanctus 0.042381433
## T_sanctus_B34946 -1.039375900 0.618823166 sanctus 0.047023209
## T_sanctus_B43266 0.455076212 0.799674015 sanctus 0.097578204
## T_sanctus_B50292 1.175622795 3.951464961 sanctus 0.083854692
## T_sanctus_B50543 0.086830128 1.958278059 sanctus 0.017860747
## T_sanctus_B51072 0.580018587 1.286692316 sanctus 0.014328961
## T_sanctus_B53055 -0.957151286 0.633320743 sanctus 0.254187689
## T_sanctus_B53068 -0.570247254 1.427888709 sanctus 0.059334006
## T_sanctus_B54673 0.231623813 1.794731702 sanctus 0.042482341
## T_sanctus_B57402 0.640068170 1.448941103 sanctus 0.190413724
## T_sanctus_B59372 -0.373745803 2.623081494 sanctus 0.008476287
## T_sanctus_B60180 3.215068103 -3.989047376 sanctus 0.255297679
## T_sanctus_B60181 4.269993134 -5.747485791 sanctus 0.085973764
## T_sanctus_B60182 3.501039271 -6.634343165 sanctus 0.010797175
## T_sanctus_B60183 4.603419044 -7.329570051 sanctus 0.019172553
## T_sanctus_B60184 4.420949020 -5.946555363 sanctus 0.011503532
## T_saurophagus_18929 0.134946906 -0.488372022 saurophagus 0.024520686
## T_saurophagus_27804 0.094509531 -0.510629865 saurophagus 0.015237134
## T_saurophagus_36179 0.092665120 -0.528368321 saurophagus 0.015539859
## T_saurophagus_36283 0.217080279 -0.389168951 saurophagus 0.251463169
## T_saurophagus_36284 0.137792886 -0.565139745 saurophagus 0.007870838
## T_saurophagus_69666 0.093721876 -0.180880885 saurophagus 0.381432896
## T_sordidus_B33717 -0.004682335 -0.331531463 sordidus 0.017860747
## T_sordidus_B33718 -0.215913545 0.065241856 sordidus 0.016548940
## T_sordidus_B33719 -0.730550289 -0.365917932 sordidus 0.135216953
## T_sordidus_B33720 -0.562784815 -0.555068407 sordidus 0.146922301
## T_sordidus_B44198 0.038921420 0.177124027 sordidus 0.131886983
## T_sordidus_B44295 0.742813349 -0.027004728 sordidus 0.069929364
## T_sordidus_B44296 0.315676735 -0.075786509 sordidus 0.161755802
## T_sordidus_B51462 0.143493047 -0.045086290 sordidus 0.076892028
## T_tristrami_18953 -0.003983793 -0.054350021 tristrami 0.030272452
## T_tristrami_27723 0.095332438 -0.270971110 tristrami 0.135721493
## T_tristrami_27752 -0.346754072 -0.119697034 tristrami 0.388092836
## T_tristrami_27792 0.428510103 -0.586606602 tristrami 0.256710394
## T_tristrami_27793 0.361864847 -0.340767726 tristrami 0.061150353
## T_tristrami_32049 -0.442321360 0.227506853 tristrami 0.030070636
## T_tristrami_33253 0.013433850 0.006098795 tristrami 0.009081736
## T_tristrami_33839 -0.813052247 1.707067864 tristrami 0.022300706
## T_tristrami_33858 0.727865546 0.713864412 tristrami 0.285771948
## T_tristrami_33864 0.301343335 2.279301422 tristrami 0.015237134
## T_tristrami_33867 -0.043567689 3.015457477 tristrami 0.017860747
## T_tristrami_33895 -0.160271635 1.211543462 tristrami 0.178607467
## T_tristrami_36188 -0.441053456 -0.197016113 tristrami 0.127951564
## T_tristrami_6704 0.098793004 -0.261303412 tristrami 0.041775984
##
## [[3]]
## PC1 PC2 PC3 PC4
## T_albicilla_22581 5.6452390 -8.41239840 -5.26281901 2.035329274
## T_albicilla_22591 5.6832063 -8.33728683 -5.24203958 1.964060555
## T_albicilla_22592 5.6831131 -8.26086973 -5.08093255 1.834000232
## T_albicilla_22611 4.0539320 -5.46903998 -3.46666627 1.380183607
## T_albicilla_85104 5.6950096 -8.38543637 -5.22059915 1.841820295
## T_albicilla_85105 5.6514486 -8.13088805 -5.07694529 1.731437790
## T_chloris_12584 2.6846536 -2.43618609 7.15034669 -5.056849236
## T_chloris_12606 2.7878221 -2.42676963 6.62837541 -5.554308113
## T_chloris_13960 2.5905652 -2.78419132 6.87121164 -8.078667197
## T_chloris_14446 2.5362635 -2.44885951 6.66128381 -7.180251996
## T_chloris_20983 2.5663595 -2.48004348 7.02702548 -7.488778660
## T_chloris_22075 2.7413150 -2.41049636 7.67349655 -5.387969736
## T_chloris_23253 2.6999684 -2.61643005 6.81559769 -4.756401022
## T_chloris_23630 2.7380806 -3.10671890 5.66416156 -7.542775187
## T_chloris_23632 2.6605392 -2.83783507 5.20594517 -6.765861129
## T_chloris_24382 2.5032655 -2.11360717 6.70102646 -4.950189873
## T_chloris_24727 2.5081048 -2.09734408 6.97947307 -4.640618985
## T_colonus_2003089 3.1443937 -3.67345991 -0.17831535 -1.166091537
## T_colonus_2003097 3.0834069 -3.50141322 0.02831708 -1.443139403
## T_colonus_2004070 3.1339628 -3.78798452 -0.87987061 -1.616569058
## T_leucopygius_32019 -28.5543271 -8.19034114 -0.57740988 0.005705525
## T_leucopygius_32037 -20.2695617 -5.96639578 -0.13225300 -0.167211416
## T_leucopygius_34505 -29.5935790 -8.42680422 -0.78681096 0.074590332
## T_leucopygius_34508 -22.6930469 -6.91718582 -0.15226248 -0.124307186
## T_leucopygius_DOT6654 -27.7871292 -8.11335368 -0.59868985 0.072632644
## T_sanctus_14877 -0.5578654 6.23810445 -1.44576024 -0.604079601
## T_sanctus_14879 -0.2962484 4.35558041 -1.09121575 -0.474037780
## T_sanctus_24565 -0.3500885 6.74262764 -1.88967712 0.180470651
## T_sanctus_25117 -0.7149583 6.19497469 -2.12784709 -0.007793604
## T_sanctus_33267 -0.6522212 6.59063409 -1.50670937 -0.228983896
## T_sanctus_34636 -0.6336239 7.19028431 -1.72124869 -0.581490192
## T_sanctus_34659 -0.2843195 4.97957835 -1.29233089 0.155135766
## T_sanctus_35549 -0.4853389 6.05294816 -1.39148974 -0.244293553
## T_sanctus_72545 -0.5153050 6.45251560 -1.60174978 0.124121799
## T_sanctus_7567 -0.6667380 7.08406971 -1.32357662 0.066595532
## T_sanctus_B29435 -0.3964496 6.17258882 -2.51088713 -0.340629738
## T_sanctus_B32637 -0.6536034 5.60635033 -1.39293920 -0.311172006
## T_sanctus_B33280 -0.7486419 6.84296250 -2.40397402 -0.257011168
## T_sanctus_B34636 -0.6984801 7.33580858 -1.88758344 -0.343291544
## T_sanctus_B34659 -1.0137437 7.25110359 -2.33732993 0.112295065
## T_sanctus_B34946 -0.5974342 6.66159533 -1.86046646 -0.261562502
## T_sanctus_B43266 -0.7086985 6.48204652 -2.18159280 0.053863580
## T_sanctus_B50292 -0.9373012 7.13993890 -1.95658421 0.098770471
## T_sanctus_B50543 -0.9138289 6.56875252 -2.15878677 -0.196626903
## T_sanctus_B51072 -0.6883753 6.71811696 -2.45402180 0.213218337
## T_sanctus_B53055 -0.4120105 5.23177019 -1.47034402 0.169967841
## T_sanctus_B53068 -0.7475792 6.17845897 -1.54354742 -0.430702482
## T_sanctus_B54673 -0.5289031 6.73179896 -1.79177139 0.368406671
## T_sanctus_B57402 -0.5652764 6.32228754 -2.08732841 0.104600591
## T_sanctus_B59372 -0.5864496 6.59083791 -1.92560723 -0.110646991
## T_sanctus_B60180 -0.6196309 6.06787861 -1.78001059 -1.000836161
## T_sanctus_B60181 -0.8673624 7.17337090 -2.18235958 -0.347033485
## T_sanctus_B60182 -0.8048558 7.27912615 -1.88117555 0.133661905
## T_sanctus_B60183 -0.3994268 7.22178366 -2.32744705 -0.322094373
## T_sanctus_B60184 -0.7719923 7.54493985 -1.14582570 -0.066485887
## T_saurophagus_18929 5.5132942 -8.04261261 -5.63566251 1.492370799
## T_saurophagus_27804 5.5214192 -8.09568247 -5.26950425 1.539493225
## T_saurophagus_36179 5.6151762 -8.38941474 -5.96067220 1.688784914
## T_saurophagus_36283 4.6658259 -7.16752488 -4.64332181 1.223193116
## T_saurophagus_36284 5.4693665 -8.15390171 -5.77216977 1.661716649
## T_saurophagus_69666 3.3525662 -4.69335973 -2.77738586 0.852616743
## T_sordidus_B33717 1.5761060 -0.13870149 9.70225414 7.948231139
## T_sordidus_B33718 1.6850676 -0.14989923 9.51437039 7.488878763
## T_sordidus_B33719 1.4483052 -0.09149056 8.95774046 7.693513421
## T_sordidus_B33720 1.2605462 -0.07077542 8.89658074 7.621189804
## T_sordidus_B44198 1.5419871 -0.32152071 8.57288555 7.102565118
## T_sordidus_B44295 1.6163416 -0.64330257 8.05555711 6.960627102
## T_sordidus_B44296 1.4596427 -0.68341290 8.38375556 6.934516010
## T_sordidus_B51462 1.6637220 -0.41529467 9.16440935 7.640017509
## T_tristrami_18953 4.7172294 -6.91514875 -2.58663475 -0.326577371
## T_tristrami_27723 4.1717161 -6.45193956 -2.43340836 -0.128146007
## T_tristrami_27752 3.1451754 -4.78831908 -1.56984250 -0.353897001
## T_tristrami_27792 3.3021500 -4.83500889 -1.19515277 -0.546426632
## T_tristrami_27793 4.2613683 -6.08006682 -1.86041957 -0.025182308
## T_tristrami_32049 4.5929769 -6.60603734 -2.16839134 -0.429173135
## T_tristrami_33253 4.5779882 -6.54607787 -2.53277078 -0.073025990
## T_tristrami_33839 -0.9543847 6.85923067 -1.68578019 0.481560667
## T_tristrami_33858 -0.3119779 4.70850068 -0.95433080 0.121307620
## T_tristrami_33864 -0.6757799 6.70611009 -1.67828205 -0.860612589
## T_tristrami_33867 -0.8177934 6.82717865 -1.60988412 0.248672051
## T_tristrami_33895 -0.7243216 6.15084225 -1.63893544 -0.579365561
## T_tristrami_36188 4.3312600 -6.37494009 -2.54459633 -0.009552161
## T_tristrami_6704 4.9187719 -7.26892518 -2.80986655 -0.039402760
## PC5 PC6 PC7 PC8
## T_albicilla_22581 -5.187871133 -1.252012984 5.868196792 1.172802662
## T_albicilla_22591 -5.475395276 -1.128759865 5.793743674 1.154487096
## T_albicilla_22592 -5.410654039 -1.136945397 5.544712352 0.992730260
## T_albicilla_22611 -3.436596619 -1.076745470 4.247722523 0.816650132
## T_albicilla_85104 -5.225230015 -1.138642082 4.962736135 0.564182901
## T_albicilla_85105 -5.143589157 -0.988940167 4.814554622 0.420048209
## T_chloris_12584 -1.073910441 6.301226302 1.381556673 -1.918244501
## T_chloris_12606 -0.919165979 5.583663708 1.904823594 -1.890576504
## T_chloris_13960 -1.989115710 -5.698881885 -1.928914277 2.987328330
## T_chloris_14446 -2.056426791 -6.011526064 -1.913209523 2.960184204
## T_chloris_20983 -2.088036289 -5.478183926 -1.906589669 3.169079048
## T_chloris_22075 -1.050603902 6.088493935 1.513835445 -1.830661999
## T_chloris_23253 -1.071593976 5.112560223 1.286828795 -1.643986041
## T_chloris_23630 -2.550228654 -4.885167773 -2.094963128 3.041897216
## T_chloris_23632 -2.481480546 -4.401558908 -1.717070754 2.644626220
## T_chloris_24382 -1.194326060 6.325748589 1.621516468 -2.087241976
## T_chloris_24727 -0.911347086 6.158017666 1.733724004 -2.038927912
## T_colonus_2003089 4.059206243 -5.472603190 0.991323177 -9.605343901
## T_colonus_2003097 3.569836845 -5.361617031 0.830047833 -9.415367393
## T_colonus_2004070 4.303180097 -5.116517779 1.174000610 -9.503447539
## T_leucopygius_32019 -0.168434108 0.021870150 0.025207383 0.062678297
## T_leucopygius_32037 0.019221328 -0.179073287 0.431639493 0.169718473
## T_leucopygius_34505 -0.114865050 0.223827695 -0.230804917 -0.055377050
## T_leucopygius_34508 -0.160703665 0.204769986 0.162172164 -0.090001484
## T_leucopygius_DOT6654 -0.200379826 -0.010336040 -0.025040845 -0.049239561
## T_sanctus_14877 -0.217208700 0.431333149 0.608908303 -0.395260844
## T_sanctus_14879 -0.304523223 -0.115839209 -0.060370963 -0.495003236
## T_sanctus_24565 -0.040539343 0.247368204 -0.189068286 0.099526651
## T_sanctus_25117 -0.141171496 0.128955346 -0.178322930 -0.088329056
## T_sanctus_33267 -0.183485960 0.125512166 -0.014672092 -0.188564599
## T_sanctus_34636 -0.465430889 0.509877157 -0.004979664 -0.071574696
## T_sanctus_34659 0.067296968 -0.448216740 -0.288492516 0.169088295
## T_sanctus_35549 -0.030866471 -0.082306717 -0.306435535 0.279440505
## T_sanctus_72545 -0.048083257 -0.012863752 0.072042681 0.590280977
## T_sanctus_7567 0.119339420 0.125721170 0.039521461 0.074364431
## T_sanctus_B29435 0.052245331 -0.288802845 -0.204215998 -0.376239933
## T_sanctus_B32637 0.068175440 0.330860039 -0.151456828 -0.195507815
## T_sanctus_B33280 -0.015624120 0.284937345 -0.291046736 0.918589761
## T_sanctus_B34636 -0.420458237 0.352086525 -0.035991582 0.010892006
## T_sanctus_B34659 0.220552451 0.027063610 -0.280865914 0.361299954
## T_sanctus_B34946 -0.190988722 0.419687731 0.009618425 0.454898412
## T_sanctus_B43266 0.067673358 0.215517473 -0.012783980 -0.311374731
## T_sanctus_B50292 -0.162942498 -0.112553991 -0.256012697 0.785284399
## T_sanctus_B50543 -0.004352241 -0.031191841 -0.209473259 -0.208793775
## T_sanctus_B51072 0.065084705 -0.224718304 0.757967590 -0.006269405
## T_sanctus_B53055 -0.405967920 0.532034142 0.418081253 0.511449284
## T_sanctus_B53068 -0.648150939 0.057614147 -0.384774110 0.647672407
## T_sanctus_B54673 -0.683073699 -0.193372469 -0.100939843 0.164717773
## T_sanctus_B57402 -0.579434870 -0.181866570 -0.085951742 0.625164190
## T_sanctus_B59372 -0.011637982 0.419671285 -0.477883906 0.951599263
## T_sanctus_B60180 0.201644708 0.061470490 0.699596042 -0.489558384
## T_sanctus_B60181 0.192273163 0.059571296 1.098574967 0.020020999
## T_sanctus_B60182 0.547881247 -0.006171584 0.409798559 -0.219801797
## T_sanctus_B60183 -0.239054192 0.384633679 0.896758369 -0.368345945
## T_sanctus_B60184 0.330240813 0.187713705 0.161062861 -0.604896978
## T_saurophagus_18929 -3.218245686 1.829348602 -6.926869936 -1.443689591
## T_saurophagus_27804 -3.623475782 1.750601397 -5.868828012 -1.399275416
## T_saurophagus_36179 -3.634958370 1.954825669 -6.895045124 -1.422188412
## T_saurophagus_36283 -2.941394644 1.604669391 -5.193523780 -1.109702518
## T_saurophagus_36284 -3.471219475 1.903295845 -6.629480668 -1.395568772
## T_saurophagus_69666 -1.935039667 0.974300899 -3.638063546 -0.326245669
## T_sordidus_B33717 0.071063847 -0.642628401 -0.222962523 0.007924132
## T_sordidus_B33718 0.009184373 -1.004820706 -0.687835214 -0.054461622
## T_sordidus_B33719 -0.236151131 -0.598265195 -0.605673098 0.228194378
## T_sordidus_B33720 -0.051496197 -0.201960926 -0.374413866 -0.149156690
## T_sordidus_B44198 -0.061776521 -0.947790668 -0.065449430 0.492931368
## T_sordidus_B44295 0.030219066 -0.673838885 -0.135114024 0.935811455
## T_sordidus_B44296 0.088415012 -0.959526166 -0.336104241 0.687395274
## T_sordidus_B51462 -0.276133384 -0.339301440 -0.441548472 0.113108000
## T_tristrami_18953 7.314117052 0.718071212 0.269303675 2.628917902
## T_tristrami_27723 5.948277198 0.981196086 0.477412506 2.241717401
## T_tristrami_27752 4.683542112 0.859718835 0.159292595 1.165263271
## T_tristrami_27792 5.317267532 0.121372233 1.017669241 1.311897481
## T_tristrami_27793 6.456514484 1.125004108 0.870682594 2.472781154
## T_tristrami_32049 7.392861892 0.503135391 -0.200569713 2.684833086
## T_tristrami_33253 7.588030614 0.835141394 -0.050682755 2.515580934
## T_tristrami_33839 -0.425729809 -0.091653563 -0.766941631 0.911439538
## T_tristrami_33858 -0.186798363 -0.595010735 -0.179071928 0.373018709
## T_tristrami_33864 -0.144920396 0.537777206 0.416176238 0.373965453
## T_tristrami_33867 -0.047364089 -0.117391202 -0.520720508 0.086795773
## T_tristrami_33895 0.380216834 -0.634635783 -0.183166104 -0.224881707
## T_tristrami_36188 6.602850878 0.704474069 0.455542287 2.846157914
## T_tristrami_6704 7.191239585 0.517500291 0.146044883 2.774671876
## PC9 PC10 pop missing
## T_albicilla_22581 0.218280865 -0.06200242 albicilla 0.019246299
## T_albicilla_22591 0.206500293 0.05967875 albicilla 0.007537012
## T_albicilla_22592 0.227380433 0.05729810 albicilla 0.016016151
## T_albicilla_22611 0.270618918 -0.02441943 albicilla 0.265545087
## T_albicilla_85104 0.157866365 0.04104670 albicilla 0.031493943
## T_albicilla_85105 0.265754851 0.05674464 albicilla 0.030955585
## T_chloris_12584 0.164203769 0.08123257 chloris 0.006729475
## T_chloris_12606 -0.063731663 0.29209332 chloris 0.022745626
## T_chloris_13960 -0.714491994 -0.32828869 chloris 0.019919246
## T_chloris_14446 -0.432151826 0.04357376 chloris 0.011574697
## T_chloris_20983 -0.646826205 -0.21226387 chloris 0.012382234
## T_chloris_22075 0.384291356 0.61233231 chloris 0.011440108
## T_chloris_23253 0.267422646 0.56224343 chloris 0.047240915
## T_chloris_23630 0.067148309 -0.12363291 chloris 0.060430686
## T_chloris_23632 0.237977087 -0.22243591 chloris 0.094481830
## T_chloris_24382 0.538039905 0.36839134 chloris 0.062718708
## T_chloris_24727 0.464376727 -0.02477160 chloris 0.110228802
## T_colonus_2003089 0.708257619 0.32452160 colonus 0.100269179
## T_colonus_2003097 0.701004867 -0.09941303 colonus 0.076312248
## T_colonus_2004070 0.814499693 0.13486173 colonus 0.107133244
## T_leucopygius_32019 0.057600545 -0.07115051 leucopygius 0.106594886
## T_leucopygius_32037 -0.253111050 0.37284323 leucopygius 0.371601615
## T_leucopygius_34505 0.022199862 -0.18129032 leucopygius 0.092328398
## T_leucopygius_34508 -0.659220776 0.04132618 leucopygius 0.300538358
## T_leucopygius_DOT6654 0.533886070 -0.28838475 leucopygius 0.140376851
## T_sanctus_14877 -6.148414644 -1.21455015 sanctus 0.030013459
## T_sanctus_14879 -1.708850136 -0.02916317 sanctus 0.330148048
## T_sanctus_24565 0.922055377 0.48996849 sanctus 0.010497981
## T_sanctus_25117 1.038178741 -0.32254842 sanctus 0.066083445
## T_sanctus_33267 2.009101313 0.29878256 sanctus 0.020053836
## T_sanctus_34636 3.888586601 -10.85882464 sanctus 0.017227456
## T_sanctus_34659 1.535323963 2.25764396 sanctus 0.229609690
## T_sanctus_35549 1.425720384 0.44593167 sanctus 0.066352624
## T_sanctus_72545 0.708625854 0.57667174 sanctus 0.032839838
## T_sanctus_7567 1.129673040 1.61702003 sanctus 0.018438762
## T_sanctus_B29435 0.153078770 0.71669814 sanctus 0.053566622
## T_sanctus_B32637 0.974244529 1.62145839 sanctus 0.200942127
## T_sanctus_B33280 2.404304370 2.34731277 sanctus 0.092193809
## T_sanctus_B34636 3.841384171 -10.81045654 sanctus 0.018169583
## T_sanctus_B34659 2.328706498 3.29425115 sanctus 0.023553163
## T_sanctus_B34946 1.331850785 -0.47942460 sanctus 0.025841184
## T_sanctus_B43266 -0.416035955 1.32928141 sanctus 0.046837147
## T_sanctus_B50292 2.428835014 3.15413651 sanctus 0.049932705
## T_sanctus_B50543 1.301963257 1.17457457 sanctus 0.017092867
## T_sanctus_B51072 0.169705831 1.70365551 sanctus 0.011305518
## T_sanctus_B53055 1.279758235 -0.57994924 sanctus 0.185464334
## T_sanctus_B53068 0.804539212 0.23140818 sanctus 0.037146703
## T_sanctus_B54673 0.392227872 1.13691549 sanctus 0.026110363
## T_sanctus_B57402 0.784842325 1.49756464 sanctus 0.115343203
## T_sanctus_B59372 2.300602522 1.56737742 sanctus 0.006325707
## T_sanctus_B60180 -4.776190890 -0.49712510 sanctus 0.169582773
## T_sanctus_B60181 -6.428820889 -1.14000183 sanctus 0.041857335
## T_sanctus_B60182 -6.472170959 -1.49111266 sanctus 0.008613728
## T_sanctus_B60183 -7.029579520 -1.19923968 sanctus 0.011440108
## T_sanctus_B60184 -5.996487561 -0.85358896 sanctus 0.009017497
## T_saurophagus_18929 -0.474336155 -0.03473073 saurophagus 0.013458950
## T_saurophagus_27804 -0.509792245 -0.11609298 saurophagus 0.007133244
## T_saurophagus_36179 -0.537234555 -0.10821649 saurophagus 0.005921938
## T_saurophagus_36283 -0.542517962 -0.13684638 saurophagus 0.174158816
## T_saurophagus_36284 -0.556998592 -0.06730314 saurophagus 0.002153432
## T_saurophagus_69666 -0.003215092 0.10187968 saurophagus 0.386944818
## T_sordidus_B33717 -0.361236315 -0.29142262 sordidus 0.012920592
## T_sordidus_B33718 -0.153431878 -0.05647432 sordidus 0.014939435
## T_sordidus_B33719 -0.237039393 -0.66568513 sordidus 0.081426649
## T_sordidus_B33720 -0.200962613 -0.64280175 sordidus 0.088425303
## T_sordidus_B44198 0.260746420 0.09649012 sordidus 0.074562584
## T_sordidus_B44295 -0.190650914 0.38323511 sordidus 0.051951548
## T_sordidus_B44296 0.045680569 0.39539206 sordidus 0.096096904
## T_sordidus_B51462 0.047079200 -0.07830341 sordidus 0.036473755
## T_tristrami_18953 0.240052074 -0.17553615 tristrami 0.017631225
## T_tristrami_27723 -0.267470617 0.01763533 tristrami 0.080619112
## T_tristrami_27752 -0.015940875 -0.16979356 tristrami 0.303499327
## T_tristrami_27792 -0.574525468 -0.12805275 tristrami 0.216419919
## T_tristrami_27793 -0.499361958 0.11628532 tristrami 0.041588156
## T_tristrami_32049 0.415561436 -0.33476624 tristrami 0.021130552
## T_tristrami_33253 0.032609399 -0.05234804 tristrami 0.006056528
## T_tristrami_33839 1.514005547 0.61558295 tristrami 0.011574697
## T_tristrami_33858 0.329704623 0.83523258 tristrami 0.204845222
## T_tristrami_33864 1.513544509 1.42010639 tristrami 0.015074024
## T_tristrami_33867 1.910056047 1.47392616 tristrami 0.008882907
## T_tristrami_33895 0.914015181 0.98036321 tristrami 0.114939435
## T_tristrami_36188 0.055514246 -0.43655638 tristrami 0.074831763
## T_tristrami_6704 0.131610608 -0.33600069 tristrami 0.023283984
#set two potential cutoffs
vcfRa<-missing_by_snp(vcfR, cutoff = .8)
## cutoff is specified, filtered vcfR object will be returned
## 87.73% of SNPs fell below a completeness cutoff of 0.8 and were removed from the VCF
vcfRb<-missing_by_snp(vcfR, cutoff = .85)
## cutoff is specified, filtered vcfR object will be returned
## 90.8% of SNPs fell below a completeness cutoff of 0.85 and were removed from the VCF
#convert each to genlight
gena<-vcfR2genlight(vcfRa)
genb<-vcfR2genlight(vcfRb)
#output pairwise difference matrix for each to run splitstree
gena@ind.names<-gsub(gena@ind.names, pattern = "T_", replacement = "")
gena@ind.names<-gsub(gena@ind.names, pattern = "_", replacement = "")
gena@ind.names<-gsub(gena@ind.names, pattern = "albicilla", replacement = "alb")
gena@ind.names<-gsub(gena@ind.names, pattern = "chloris", replacement = "chlor")
gena@ind.names<-gsub(gena@ind.names, pattern = "colonus", replacement = "col")
gena@ind.names<-gsub(gena@ind.names, pattern = "sanctus", replacement = "san")
gena@ind.names<-gsub(gena@ind.names, pattern = "saurophagus", replacement = "saur")
gena@ind.names<-gsub(gena@ind.names, pattern = "sordidus", replacement = "sord")
gena@ind.names<-gsub(gena@ind.names, pattern = "tristrami", replacement = "tris")
gena@ind.names<-gsub(gena@ind.names, pattern = "leucopygius", replacement = "leu")
gena@ind.names<-gsub(gena@ind.names, pattern = "DOT", replacement = "D")
gena@ind.names
## [1] "alb22581" "alb22591" "alb22592" "alb22611" "alb85104"
## [6] "alb85105" "chlor12584" "chlor12606" "chlor13960" "chlor14446"
## [11] "chlor20983" "chlor22075" "chlor23253" "chlor23630" "chlor23632"
## [16] "chlor24382" "chlor24727" "col2003089" "col2003097" "col2004070"
## [21] "leu32019" "leu32037" "leu34505" "leu34508" "leuD6654"
## [26] "san14877" "san14879" "san24565" "san25117" "san33267"
## [31] "san34636" "san34659" "san35549" "san72545" "san7567"
## [36] "sanB29435" "sanB32637" "sanB33280" "sanB34636" "sanB34659"
## [41] "sanB34946" "sanB43266" "sanB50292" "sanB50543" "sanB51072"
## [46] "sanB53055" "sanB53068" "sanB54673" "sanB57402" "sanB59372"
## [51] "sanB60180" "sanB60181" "sanB60182" "sanB60183" "sanB60184"
## [56] "saur18929" "saur27804" "saur36179" "saur36283" "saur36284"
## [61] "saur69666" "sordB33717" "sordB33718" "sordB33719" "sordB33720"
## [66] "sordB44198" "sordB44295" "sordB44296" "sordB51462" "tris18953"
## [71] "tris27723" "tris27752" "tris27792" "tris27793" "tris32049"
## [76] "tris33253" "tris33839" "tris33858" "tris33864" "tris33867"
## [81] "tris33895" "tris36188" "tris6704"
pop(gena)<-popmap$pop
sample.div.80 <- stamppNeisD(gena, pop = FALSE)
#export for splitstree
#stamppPhylip(distance.mat=sample.div.80, file="~/Desktop/todi.2022/todi.80.splits.txt")
#80% completeness cutoff splitstree
knitr::include_graphics(c("/Users/devder/Desktop/todi.2022/todi.80.splitstree.png"))
#repeat for 85% cutoff
#output pairwise difference matrix for each to run splitstree
genb@ind.names<-gena@ind.names
pop(genb)<-popmap$pop
sample.div.85 <- stamppNeisD(genb, pop = FALSE)
#export for splitstree
#stamppPhylip(distance.mat=sample.div.85, file="~/Desktop/todi.2022/todi.85.splits.txt")
#85% completeness cutoff splitstree
knitr::include_graphics(c("/Users/devder/Desktop/todi.2022/todi.85.splitstree.png"))
#repeat with removing singletons
vcfR.mac<-min_mac(vcfRa, min.mac = 2)
## 28.31% of SNPs fell below a minor allele count of 2 and were removed from the VCF
genc<-vcfR2genlight(vcfR.mac)
genc@ind.names<-gena@ind.names
pop(genc)<-popmap$pop
sample.div <- stamppNeisD(genc, pop = FALSE)
#export for splitstree
#stamppPhylip(distance.mat=sample.div, file="~/Desktop/todi.2022/todi.80.min.mac.splits.txt")
#80% completeness cutoff with min.mac splitstree
knitr::include_graphics(c("/Users/devder/Desktop/todi.2022/todi.80.mac.splitstree.png"))
#the three splitstrees are nearly identical. I am satisfied that neither missing data nor singletons are driving patterns of sample relatedness/assignment. We will keep the 85% complete dataset without a minor allele filter for downstream analyses because it looks the cleanest.
#plot depth per snp and per sample
dp <- extract.gt(vcfRa, element = "DP", as.numeric=TRUE)
heatmap.bp(dp, rlabels = FALSE)
#plot genotype quality per snp and per sample
gq <- extract.gt(vcfRa, element = "GQ", as.numeric=TRUE)
heatmap.bp(gq, rlabels = FALSE)
###We can use the convenient function ‘write.vcf’ from vcfR to export our filtered vcf file for downstream analyses
#write out vcf
vcfR::write.vcf(vcfRb, file = "~/Desktop/todi.2022/todi.85.vcf.gz")
#perform linkage filtering to get a reduced vcf with only unlinked SNPs
vcfR.thin<-distance_thin(vcfRb, min.distance = 100)
##
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## 1892 out of 7430 input SNPs were not located within 100 base-pairs of another SNP and were retained despite filtering
vcfR.thin
## ***** Object of Class vcfR *****
## 83 samples
## 32 CHROMs
## 1,892 variants
## Object size: 12.1 Mb
## 8.083 percent missing data
## ***** ***** *****
vcfR::write.vcf(vcfR.thin, file = "~/Desktop/todi.2022/todi.unlinked.85.vcf.gz")